CHAPTER 3 - THE MOLECUL

ES of life

WHAT WE EAT!

And..What we fart!

ORGANIC COMPOUNDS Organic Compounds contain

Carbon. Carbon is an important element

because… It forms 4 bonds.Tends to form strong

covalent bonds.

Can combine to form: single, double & triple bonds as

well as chains branches and rings.

ORGANIC COMPOUNDS

We will practice buildingthese today!

Functional groups help determine properties of organic compoundsAll are polar because oxygen or

nitrogen exert a strong pull on shared electrons

Polarity tends to make these molecules hydrophilic (water-loving)A necessity for life!

ORGANIC COMPOUNDS

TABLE 3.2 FUNCTIONAL GROUPS OF ORGANIC COMPOUNDS X

FUNCTIONAL GROUPS Activity 3B – online textbook

There are 4 major categories of organic compounds:

CarbohydratesLipidsProteinsNucleic Acids

ORGANIC COMPOUNDS

MACROMOLECULES

Carbohydrates, Lipids, Proteins and Nucleic Acids are macromolecules.

This means they are BIG molecules.

They are made of smaller molecules that serve as the building blocks.

Like a brick is the building block for a brick wall these smaller molecules combine to create the macromolecules.

ORGANIC COMPOUNDS

Smaller Molecules (Building Blocks/subunits)

= monomers

Larger Molecules

= polymers

ORGANIC COMPOUNDS

MAKING & BREAKING POLYMERS

Condensation Reaction /Dehydration Synthesis

Hydrolysis Reaction

Monomer Polymer

Remove water

Add water

DEHYDRATION SYNTHESIS

Removing water to build a polymer

HYDROLYSIS

Adding water to break down a polymer

CARBOHYDRATES Why does our body (and all

living things) need this molecule?Provides ENERGY

Where do we get this molecule?Pasta, Potatoes, Rice, Candy,

Soda, Sugar

CARBOHYDRATES

Which is the polymer and which is the monomer?

Polymer!

Monomer!

CARBOHYDRATES Monomers of carbs =

monosaccharideMono means 1, saccharide

means sugarCommon examples are:

Glucose (grains)Fructose (fruit)Galactose (milk)

FIGURE 3.4B STRUCTURES OF GLUCOSE AND FRUCTOSE

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H H

H

H

H

HO

H

H

H

C

O

HO

OH

OH

OH

OH

OH

OH

OH

C O

OH

Glucose Fructose

COUNT UP THE ATOMS FOR EACH

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H H

H

H

H

HO

H

H

H

C

O

HO

OH

OH

OH

OH

OH

OH

OH

C O

OH

Glucose Fructose

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H H

H

H

H

HO

H

H

H

C

O

HO

OH

OH

OH

OH

OH

OH

OH

C O

OH

Glucose Fructose

Glucose Fructose

Carbon 6 6

Hydrogen 12 12

Oxygen 6 6

ISOMERS – SAME MOLECULAR FORMULA, DIFFERENT STRUCTURAL FORMULA

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H H

H

H

H

HO

H

H

H

C

O

HO

OH

OH

OH

OH

OH

OH

OH

C O

OH

Glucose Fructose

FIGURE 3.4C THREE REPRESENTATIONS OF THE RING FORM OF GLUCOSE

H

H

H

H

H

H H

H

HH

O

C

C

C C

O

OH

OH HO OH

OH

CH2OH

CH2OH

C

OH

OH

O

OH

Structural formula

Abbreviated structure

Simplified structure

6

5

4

3 2

1

CARBOHYDRATES

Functional GroupsFunctional groups are groups of

atoms that give a molecule its characteristic properties.

Carbohydrates have 2 functional groups =

Hydroxyl -OH

Carbonyl -COH

CARBOHYDRATES

• Here you see 2 monosaccharides coming together to form a disaccharide.

What type of reaction is this?

_______________________________Dehydration synthesis or condensation reaction

CARBOHYDRATES

Polymers = Dissaccharide (two)

Common examples are:Sucrose - sugarMaltose – grains (beer)

Lactose - milk

Lactose

TABLE 3.6 SWEETNESS SCALE

Polysaccharide (many)Common examples are:

Starch - potatoCellulose – plant cell walls

Glycogen - animals

CARBOHYDRATES

FIGURE 3.7 POLYSACCHARIDES

Starch granules in potato tuber cells

Glycogen granules in muscle tissue

Cellulose fibrils in a plant cell wall

Glucose monomer

Cellulose molecules

STARCH

GLYCOGEN

CELLULOSE

O O

OOOOOO

O O O

O

OO

OO

OO

OO

OO

OO

O

OO

OO

OO

OO O

OOOOOO

OOOOOO

O

OH

OH

BENEDICT’S TESTFOR MONOSACCHARIDES

- +

IODINE TEST FOR POLYSACCHARIDES

MAKING & BREAKING POLYMERS

Remove WaterCondensation Reaction /Dehydration Synthesis

Monomer Polymer

Add WaterHydrolysis Reaction

LIPIDS Why does our body (and all living things)

need this molecule?Stores ENERGY Insulation & ProtectionMake up cell membranes (provide

boundaries) Where do we get this molecule?

Dairy products, Meat, Oil

LIPIDS

Triglyceride

LIPIDS Monomers

GlycerolFatty Acids

Saturated Fatty AcidsAll Single BondsFound in animalsSolid at room temperature

Unsaturated Fatty AcidsAt least 1 double or triple bondFound in plantsLiquid at room temperature

Animation

HYDROGENATED OILS To convert an oil into a solid at room

temp.Add hydrogensDecreases the number of double bonds

LIPIDS

Functional Groups = Hydroxyl Carboxyl

LIPIDS• Here you see 2

glycerol combining with a fatty acid in a dehydration reaction. This happens 3 times to create a triglyceride.

• animation

LIPIDS Polymers =

Are very diverse BUT they are all hydrophobic

Examples; Triglyceride Steroids Wax Phospholipids

FIGURE 3.9 CHOLESTEROL, A STEROID

HO

CH3

CH3

H3C CH3

CH3

A steroid – cholesterol. A molecule that is needed for cell membrane stability. Excess cholesterol due to consumption of fatty foods can lead to health problems like atherosclerosis (clogging of the arteries)

ANABOLIC STEROIDS Synthetic variants of male hormone –

testosterone Anabolism – building of substances by the

body Mimics testosterone which builds muscle

tissue

Overdosing – leads to serious side effects- depression, liver damage, shrunken

testicles, breast development

FIGURE 3.8A WATER BEADING ON THE NATURALLY OILY COATING OF FEATHERS

Drop each food sample onto a paper bag. Hold up to the light, it will turn translucent if lipids are present.

Sudan red is lipid soluble. The sudan red will stain the lipid layer. Solid red.

SUDAN RED TEST FOR LIPIDS

- +

PROTEINS Why does our body (and all

living things) need this molecule?

oMake up our structure (actin in muscles, hemoglobin and antibodies in blood, etc)

FIGURE 3.11 STRUCTURAL AND CONTRACTILE PROTEINS

PROTEINSR

ate

of r

eact

ion

Temperature (C)

0 20 40 60 80 100

Enzyme A Enzyme B

• Speed up chemical reactions (enzymes)

PROTEINS

Where do we get this molecule?Dairy products, Meat, Beans, Nuts

PROTEIN Monomers

Amino AcidsThere are only 20 different amino acids

PROTEINS

PROTEIN Functional Groups =

Amino – NH2

Carboxyl - COOH

AMINO ACID STRUCTURE

Fig. 3.14, p. 42

tyrosine (tyr) lysine (lys) glutamate (glu) glycine (gly)

UNCHARGED,POLAR AMINO ACID

POSITIVELY CHARGED,POLAR AMINO ACID

NEGATIVELY CHARGED,POLAR AMINO ACID

valine (val) phenylalanine (phe) methionine (met) proline (pro)

PROTEINS• Here you see 2 amino acids

combining in a dehydration reaction.

• Animation

Fig. 3.15, p. 43

newly formingpolypeptidechain

Onepeptidegroup

Fig. 3.17, p. 44

PROTEINS Polymers = Polypeptides

Poly means many, peptide comes from the bonding

Fig. 3.16, p. 43

disulfide bridges

PROTEINS The shape of a protein determines its

function.

Shape depends on the interaction of the R groups of each amino acid forming weak H bonds.

Because H bonds are weak they can be broken by exposure to extreme pH or temperature, and certain chemicals like salt.

When a proteins shape is altered and therefore it stops functioning correctly we say it has been denatured.

FIGURE 3.14 PROTEIN STRUCTURE – 4 LEVELSLevels of Protein Structure

Primary structureGly

ThrGly Glu

Ser Lys

Cys

ProLeu Met

Val

Lys

ValLeu Asp Ala Val Arg Gly Ser

Pro

Ala

Ile

Asn ValAla

ValHis Val

Secondary structure

C

N

O C

C

N H

O C

C

H

Hydrogenbond

O C

N HC

CO

N H

O C

C

N H

C

N

O C

C

N HO C

C

N H

CO

C

H

N H

CO

H C R

HN

Alpha helix

Amino acids

CN

H

C C

H HO

NR C C

ON

H

O

C C N

H

C C

O

N

H

O

C C NH

C

O

C N

H

O

C C N

H

C

O

O

CC

N

H

C C

O

N

H

C C

O

N

H

CC

O

N

H

CC

O

N

H

C C

O

N

H

CC

O

N

H

CC

O

H

N

C

Pleated sheet

Tertiary structure Polypeptide(single subunitof transthyretin)

Quaternary structureTransthyretin, withfour identicalPolypeptide subunits

PheArg

c) Tertiary structure of one polypeptide chain. The 3 D shape created by interactions of R groups.

A well known example is hemoglobin, which consists of 2 alpha and 2 beta chains, consisting of 141 and 146 amino acid residues respectively.

Fig. 3.18, p. 44

betachain

betachain

alphachain

hemegroup

twists andcoils in thepolypeptidechain of aglobinmolecule

alphachain

FIGURE 3.14 PROTEIN STRUCTURE – 4 LEVELSLevels of Protein Structure

GlyThr

Gly GluSer Lys

Cys

ProLeu Met

Val

Lys

ValLeu Asp Ala Val Arg Gly Ser

Pro

Ala

Ile

Asn ValAla

ValHis Val

Weak hydrogen and ionic bonds

C

N

O C

C

N H

O C

C

H

Hydrogenbond

O C

N HC

CO

N H

O C

C

N H

C

N

O C

C

N HO C

C

N H

CO

C

H

N H

CO

H C R

HN

Alpha helix

Amino acids

CN

H

C C

H HO

NR C C

ON

H

O

C C N

H

C C

O

N

H

O

C C NH

C

O

C N

H

O

C C N

H

C

O

O

CC

N

H

C C

O

N

H

C C

O

N

H

CC

O

N

H

CC

O

N

H

C C

O

N

H

CC

O

N

H

CC

O

H

N

C

Pleated sheet

Hydrogen, ionic, and disulfide bridges

Polypeptide(single subunitof transthyretin)

Not all reach this structureTransthyretin, withfour identicalPolypeptide subunits

PheArg

Covalent bonds - peptide

APPLICATION IN SCIENCE Proteins are the keys to the mysteries of

how our bodies function. Research biologists explore the shapes

of proteins and how they work A huge area of protein chemistry is in

the medical fieldAntibodies to fight infections, disease,

cancersProteins that do not function properly in

human beings with disease

http://www.ebi.ac.uk/pdbe-apps/quips?story=Sunhats

http://www.ebi.ac.uk/pdbe-apps/quips?story=XmasFactor

BIURETS TEST FOR PROTEINS

FIGURE 3.15 LINUS PAULING WITH A MODEL OF THE ALPHA HELIX IN 1948

#4) NUCLEIC ACIDS Why does our body (and all living

things) need this molecule?Stores and expresses the directions

for how to make proteinsAKA: the blueprint for life

Where do we get this molecule?We inherit this molecule from our

parents and find it in all of the foods we eat.

NUCLEIC ACIDS

NUCLEIC ACIDS

Monomers Nucleotides

3 parts

FIGURE 3.16B PART OF A POLYNUCLEOTIDE

Sugar-phosphatebackbone

T

G

C

T

A Nucleotide

FIGURE 3.16C DNA DOUBLE HELIX

C

TA

GC

C G

T A

C G

A T

A

G C

A T

A T

T A

Basepair

T

FORMING NUCLEOTIDES

… OH + H H

Short polymer Monomer

H2O

H2O

Dehydration

Hydrolysis…

Longer polymer

H

NUCLEIC ACIDS Cellular energy - ATP

NUCLEIC ACIDS Polymers =

DNA Deoxyribose Sugar Bases: A, C, G, and T

RNA Ribose Sugar Bases: A, C, G, and U